Nodal Root Angle Research Articles

Multi-locus genome-wide association study reveal genomic regions underlying root system architecture traits in Ethiopian sorghum germplasm.

The identification of genomic regions underlying the root system architecture (RSA) is vital for improving crop abiotic stress tolerance. To improve sorghum (Sorghum bicolor L. Moench) for environmental stress tolerance, information on genetic variability and genomic regions linked to RSA traits is paramount. The aim of this study was, therefore, to investigate common quantitative trait nucleotides (QTNs) via multiple methodologies and identify genomic regions linked to RSA traits in a panel of 274 Ethiopian sorghum accessions. Multi-locus genome-wide association study was conducted using 265,944 high-quality single nucleotide polymorphism markers. Considering the QTN detected by at least three different methods, a total of 17 reliable QTNs were found to be significantly associated with root angle, number, length, and dry weight. Four QTNs were detected on chromosome SBI-05, followed by SBI-01 and SBI-02 with three QTNs each. Among the 17 QTNs, 11 are colocated with previously identified root traits quantitative trait loci and the remaining six are genome regions with novel genes. A total of 118 genes are colocated with these up- and down-streams of the QTNs. Moreover, five QTNs were found intragenic. These QTNs are S5_8994835 (number of nodal roots), S10_55702393 (number of nodal roots), S1_56872999 (nodal root angle), S9_1212069 (nodal root angle), and S5_5667192 (root dry weight) intragenic regions of Sobic.005G073101, Sobic.010G198000, Sobic.001G273000, Sobic.009G013600, and Sobic.005G054700, respectively. Particularly, Sobic.005G073101, Sobic.010G198000, and Sobic.009G013600 were found responsible for the plant growth hormone-induced RSA. These genes may regulate root development in the seedling stage. Further analysis on these genes might be important to explore the genetic structure of RSA of sorghum.

Genetic dissection of root architecture in Ethiopian sorghum landraces.

This study quantified genetic variation in root system architecture (root number, angle, length and dry mass) within a diversity panel of 1771 Ethiopian sorghum landraces and identified 22 genomic regions associated with the root variations. The root system architecture (RSA) of crop plants influences adaptation to water-limited conditions and determines the capacity of a plant to access soil water and nutrients. Four key root traits (number, angle, length and dry mass) were evaluated in a diversity panel of 1771 Ethiopian sorghum landraces using purpose-built root chambers. Significant genetic variation was observed in all studied root traits, with nodal root angle ranging from 16.4° to 26.6°, with a high repeatability of 78.9%. Genome wide association studies identified a total of 22 genomic regions associated with root traits which were distributed on all chromosomes except chromosome SBI-10. Among the 22 root genomic regions, 15 co-located with RSA trait QTL previously identified in sorghum, with the remaining seven representing novel RSA QTL. The majority (85.7%) of identified root angle QTL also co-localized with QTL previously identified for stay-green in sorghum. This suggests that the stay-green phenotype might be associated with root architecture that enhances water extraction during water stress conditions. The results open avenues for manipulating root phenotypes to improve productivity in abiotic stress environments via marker-assisted selection.

Spatio-temporal distribution of water and phosphorus determine growth of sorghum genotypes with contrasting nodal root angle

Abstract Aims Increased subsoil water extraction through breeding of ‘designer’ root system architecture (RSA) may improve crop performance and resilience in the face of climate change (i.e. changing seasonal rainfall patterns). However, in many dryland environments, root systems face both water and nutrient scarcity (e.g. phosphorus (P)), with both resources often heterogeneously distributed in space and time. Under these conditions, interactions among RSA, nutrient distribution and soil water will determine crop performance, but remain poorly understood. Methods We grew two sorghum (Sorghum bicolor) genotypes defined by contrasting RSA (narrow or wide nodal root angle) in prepared soil cores with heterogeneous distributions of P and water along the soil profile. Plant growth and water use, shoot biomass, P uptake and root distribution were quantified in response to the different water × P combinations. Results Soil P placement and soil water distribution interactively determined plant growth and development in a genotype-dependent manner. The two sorghum genotypes shared common responses to P and water availability though varied for root and shoot traits and their relative responses to combined P and water stress. Conclusions Plant responses to the different water × P combinations were illustrative of the occurrence of spatio-temporal trade-offs between root architecture and efficient soil resource capture. The results suggest that the relative ability of crop root systems to effectively exploit soil profiles with greater resource availability will not necessarily be important for crop productivity in heterogeneous soil systems. Local environmental constraints should be considered when deploying genotypes with selected root architectural traits.

Differences in Root Morphologies of Contrasting Wheat (Triticum aestivum) Genotypes Are Robust of a Drought Treatment

We aimed to assess the effect of water deprivation on root traits and to establish if the wheat cultivars Spica and Maringa would be useful as parental germplasm for a genetic analysis of root traits. Plants were grown in two markedly different soils under well-watered and water-limited treatments in controlled environment growth cabinets. The drought treatment was imposed as a gradual depletion of water over 28 days as seedlings grew from a defined starting moisture content. The root traits analyzed included length, nodal root number, thickness and nodal root angle. The relative differences in traits between genotypes generally proved to be robust in terms of water treatment and soil type. Maringa had a shallower nodal root angle than Spica, which was driven by the nodal roots. By contrast, the seminal roots of Maringa were found to be similar to or even steeper than those of Spica. We conclude that the differences in root traits between Spica and Maringa were robust to the drought treatment and soil types. Phenotyping on well-watered soil is relevant for identifying traits potentially involved in conferring water use efficiency. Furthermore, Spica and Maringa are suitable parental germplasm for developing populations to determine the genetics of key root traits.

Integrated root phenotypes for improved rice performance under low nitrogen availability.

Greater nitrogen efficiency would substantially reduce the economic, energy and environmental costs of rice production. We hypothesized that synergistic balancing of the costs and benefits for soil exploration among root architectural phenes is beneficial under suboptimal nitrogen availability. An enhanced implementation of the functional–structural model OpenSimRoot for rice integrated with the ORYZA_v3 crop model was used to evaluate the utility of combinations of root architectural phenes, namely nodal root angle, the proportion of smaller diameter nodal roots, nodal root number; and L‐type and S‐type lateral branching densities, for plant growth under low nitrogen. Multiple integrated root phenotypes were identified with greater shoot biomass under low nitrogen than the reference cultivar IR64. The superiority of these phenotypes was due to synergism among root phenes rather than the expected additive effects of phene states. Representative optimal phenotypes were predicted to have up to 80% greater grain yield with low N supply in the rainfed dry direct‐seeded agroecosystem over future weather conditions, compared to IR64. These phenotypes merit consideration as root ideotypes for breeding rice cultivars with improved yield under rainfed dry direct‐seeded conditions with limited nitrogen availability. The importance of phene synergism for the performance of integrated phenotypes has implications for crop breeding.

Depiction of Genomic Regions and Genes Related with Drought Tolerance in Sorghum [Sorghum bicolor (L.) Moench

The study of quantitative trait loci (QTLs) can bridge the gap between traditional breeding procedures and more efficient genetic improvements. The study of quantitative trait loci (QTLs) can bridge the gap between traditional breeding procedures and more efficient genetic improvements. In this report, we assess progress in mapping quantitative trait loci and genes associated with drought resistance in sorghum. Drought avoidance is linked to a number of morphological and physiological adaptations, including limiting water loss and increasing water absorption. The effects of physiological parameters will be investigated in order to find certain selection criteria that could be relevant in the development of drought-tolerant genotypes. Drought avoidance is linked to a number of morphological and physiological adaptation traits, including In grain sorghum, quantitative trait loci affecting green retention are an important feature for post blooming drought tolerance that have been investigated in various situations and with various genetic backgrounds. The two QTLs remain green (Stg2 and Stg4) of B35 x Tx7000 RILs were entirely matched in both populations, according to QTL analysis performed in the two mapping populations of recombinant inbred lines (RILs). Investigation done on different 44 sorghum lines confirmed that four QTL root nodal root angle discovered in the mapping population. Significant marker–trait association’s delignated within the quantitative chromosome (CI) for root angle (qRA2_5, qRA1_8 and qRA1_10) or closely allied to root angle (qRA1_5). Post-flowering drought response is expressed in sorghum when moisture stress occurs during grain development (GS-3). Three QTLs were detected for flowering time on chromosomes 2, 6, and 9, with log odds values (LOD) ranging from 2.5 to 3.3 and explained phenotypic variance (PVE) values calculated from 6 to 11%.

Root and canopy traits and adaptability genes explain drought tolerance responses in winter wheat.

Bread wheat (Triticum aestivum L) is one of the three main staple crops worldwide contributing 20% calories in the human diet. Drought stress is the main factor limiting yields and threatening food security, with climate change resulting in more frequent and intense drought. Developing drought-tolerant wheat cultivars is a promising way forward. The use of holistic approaches that include high-throughput phenotyping and genetic markers in selection could help in accelerating genetic gains. Fifty advanced breeding lines were selected from the CIMMYT Turkey winter wheat breeding program and studied under irrigated and semiarid conditions in two years. High-throughput phenotyping was done for wheat crown root traits and canopy senescence dynamics using vegetation indices (green area using RGB images and Normalized Difference Vegetation Index using spectral reflectance). In addition, genotyping by KASP markers for adaptability genes was done. Overall, under semiarid conditions yield reduced by 3.09 t ha-1 (-46.8%) compared to irrigated conditions. Genotypes responded differently under drought stress and genotypes 39 (VORONA/HD24-12//GUN/7/VEE#8//…/8/ALTAY), 18 (BiII98) and 29 (NIKIFOR//KROSHKA) were the most drought tolerant. Root traits including shallow nodal root angle under irrigated conditions and root number per shoot under semiarid conditions were correlated with increased grain yield. RGB based vegetation index measuring canopy green area at anthesis was better correlated with GY than NDVI was with GY under drought. The markers for five established functional genes (PRR73.A1 –flowering time, TEF-7A –grain size and weight, TaCwi.4A - yield under drought, Dreb1- drought tolerance, and ISBW11.GY.QTL.CANDIDATE- grain yield) were associated with different drought-tolerance traits in this experiment. We conclude that–genotypes 39, 18 and 29 could be used for drought tolerance breeding. The trait combinations of canopy green area at anthesis, and root number per shoot along with key drought adaptability makers (TaCwi.4A and Dreb1) could be used in screening drought tolerance wheat breeding lines.

Root phenotypes of young wheat plants grown in controlled environments show inconsistent correlation with mature root traits in the field.

Using a field to lab approach, mature deep-rooting traits in wheat were correlated to root phenotypes measured on young plants from controlled conditions. Mature deep-rooting root traits of 20 wheat genotypes at maturity were established via coring in three field trials across 2 years. Field traits were correlated to phenotypes expressed by the 20 genotypes after growth in four commonly used lab screens: (i) soil tubes for root emergence, elongation, length, and branching at four ages to 34 days after sowing (DAS); (ii) paper pouches 7 DAS and (iii) agar chambers for primary root (PR) number and angles at 8 DAS; and (iv) soil baskets for PR and nodal root (NR) number and angle at 42 DAS. Correlations between lab and field root traits (r2=0.45-0.73) were highly inconsistent, with many traits uncorrelated and no one lab phenotype correlating similarly across three field experiments. Phenotypes most positively associated with deep field roots were: longest PR and NR axiles from the soil tube screen at 20 DAS; and narrow PR angle and wide NR angle from soil baskets at 42 DAS. Paper and agar PR angles were positively and significantly correlated to each other, but only wide outer PRs in the paper screen correlated positively to shallower field root traits. NR phenotypes in soil baskets were not predicted by PR phenotypes in any screen, suggesting independent developmental controls and value in measuring both root types in lab screens. Strong temporal and edaphic effects on mature root traits, and a lack of understanding of root trait changes during plant development, are major challenges in creating controlled-environment root screens for mature root traits in the field.

Dissecting root trait variability in maize genotypes using the semi-hydroponic phenotyping platform

The production of maize (Zea mays L.) is restricted by various edaphic stresses, including drought and low-fertility soil. Searching for genotypes with optimal root traits is a promising practice when breeding for improved adaptation to abiotic stress and resource-use efficiency. Using an established semi-hydroponic phenotyping technique, we assessed root trait variability across 174 maize genotypes including 113 cultivars and 11 breeding lines from northern China and 50 Serbian hybrids. Large variation in root architecture traits was observed among the tested genotypes 28 days after transplanting. Sixteen of the characterized traits had coefficients of variation greater than 0.25, especially local root traits. Root traits including total root length, root length at various depths, total shoot mass and nodal root angle, should be considered in maize breeding programs. Genotype ranking data based on a composite score was used to assist in the selection of genotypes with contrasting root architecture traits for future studies. This study identified genotypic variation in root architecture traits in a diverse genotypes of maize. The outcomes of this study could form a basis for maize breeding programs aimed at producing maize cultivars for improved adaptation to target environments.

Development of a phenotyping platform for high throughput screening of nodal root angle in sorghum

BackgroundIn sorghum, the growth angle of nodal roots is a major component of root system architecture. It strongly influences the spatial distribution of roots of mature plants in the soil profile, which can impact drought adaptation. However, selection for nodal root angle in sorghum breeding programs has been restricted by the absence of a suitable high throughput phenotyping platform. The aim of this study was to develop a phenotyping platform for the rapid, non-destructive and digital measurement of nodal root angle of sorghum at the seedling stage.ResultsThe phenotyping platform comprises of 500 soil filled root chambers (50 × 45 × 0.3 cm in size), made of transparent perspex sheets that were placed in metal tubs and covered with polycarbonate sheets. Around 3 weeks after sowing, once the first flush of nodal roots was visible, roots were imaged in situ using an imaging box that included two digital cameras that were remotely controlled by two android tablets. Free software (openGelPhoto.tcl) allowed precise measurement of nodal root angle from the digital images. The reliability and efficiency of the platform was evaluated by screening a large nested association mapping population of sorghum and a set of hybrids in six independent experimental runs that included up to 500 plants each. The platform revealed extensive genetic variation and high heritability (repeatability) for nodal root angle. High genetic correlations and consistent ranking of genotypes across experimental runs confirmed the reproducibility of the platform.ConclusionThis low cost, high throughput root phenotyping platform requires no sophisticated equipment, is adaptable to most glasshouse environments and is well suited to dissect the genetic control of nodal root angle of sorghum. The platform is suitable for use in sorghum breeding programs aiming to improve drought adaptation through root system architecture manipulation.

Genetic variation in seminal and nodal root angle and their association with grain yield of maize under water-stressed field conditions

Root angles are widely recognized to play an important role in determining rooting depth and drought tolerance in crop plants. But there has been no report revealing any association between root angle and yield performance under drought conditions in maize. There is also no simple method available to screen root angles. The objectives of this study were to evaluate genetic variation in seminal and nodal root angles in maize in greenhouse condition and their association with drought tolerance in field condition. Eighteen hybrids, of which nine were higher-yielding and nine were lower-yielding under water-stressed condition in field, were evaluated for root angle variation. Root angle was estimated as the distance between the horizontal soil surface line and slope of the root at 2 cm position from root base using a protractor. Significant phenotypic variation was observed among hybrids for seminal and nodal root angles and primary root diameter. These root traits showed strong positive correlations with grain yield under drought condition. All the higher-yielding hybrids had steeper root growth angle than the lower-yielding hybrids. A strong correlation between seminal and nodal root angles was observed. A strong correlation was also observed between 5th and 4th node nodal root angles. Either seminal or nodal root angle could be used for selection for the improvement drought tolerance. The current screening system for root angle is simple and inexpensive, and could be used for screening a large number of genotypes.

Genetic control of nodal root angle in sorghum and its implications on water extraction

Genotypic variability in root system architecture has been associated with root angle of seedlings and water extraction patterns of mature plants in a range of crops. The potential inclusion of root angle as a selection criterion in a sorghum breeding program requires (1) availability of an efficient screening method, (2) presence of genotypic variation with high heritability, and (3) an association with water extraction pattern. The aim of this study was to determine the feasibility for inclusion of nodal root angle as a selection criterion in sorghum breeding programs. A high-throughput phenotypic screen for nodal root angle in young sorghum plants has recently been developed and has been used successfully to identify significant variation in nodal root angle across a diverse range of inbred lines and a mapping population. In both cases, heritabilities for nodal root angle were high. No association between nodal root angle and plant size was detected. This implies that parental inbred lines could potentially be used to asses nodal root angle of their hybrids, although such predictability is compromised by significant interactions. To study effects of nodal root angle on water extraction patterns of mature plants, four inbred lines with contrasting nodal root angle at seedling stage were grown until at least anthesis in large rhizotrons. A consistent trend was observed that nodal root angle may affect the spatial distribution of root mass of mature plants and hence their ability to extract soil water, although genotypic differences were not significant. The potential implications of this for specific adaptation to drought stress are discussed. Results suggest that nodal root angle of young plants can be a useful selection criterion for specific drought adaptation, and could potentially be used in molecular breeding programs if QTLs for root angle can be identified.

QTL for nodal root angle in sorghum (Sorghum bicolor L. Moench) co-locate with QTL for traits associated with drought adaptation

Nodal root angle in sorghum influences vertical and horizontal root distribution in the soil profile and is thus relevant to drought adaptation. In this study, we report for the first time on the mapping of four QTL for nodal root angle (qRA) in sorghum, in addition to three QTL for root dry weight, two for shoot dry weight, and three for plant leaf area. Phenotyping was done at the six leaf stage for a mapping population (n=141) developed by crossing two inbred sorghum lines with contrasting root angle. Nodal root angle QTL explained 58.2% of the phenotypic variance and were validated across a range of diverse inbred lines. Three of the four nodal root angle QTL showed homology to previously identified root angle QTL in rice and maize, whereas all four QTL co-located with previously identified QTL for stay-green in sorghum. A putative association between nodal root angle QTL and grain yield was identified through single marker analysis on field testing data from a subset of the mapping population grown in hybrid combination with three different tester lines. Furthermore, a putative association between nodal root angle QTL and stay-green was identified using data sets from selected sorghum nested association mapping populations segregating for root angle. The identification of nodal root angle QTL presents new opportunities for improving drought adaptation mechanisms via molecular breeding to manipulate a trait for which selection has previously been very difficult.

Genetic Variability and Control of Nodal Root Angle in Sorghum

Sorghum [Sorghum bicolor (L.) Moench] is a major dryland cereal crop in environments with low and unpredictable rainfall. Root angle at the seedling stage can potentially influence root architecture and hence adaptation to drought. The aims of this study were to investigate the extent of genetic variation in nodal root angle of sorghum and to quantify the general combining ability (GCA) and specific combining ability (SCA) for the trait. A diverse range of inbred lines and hybrids was grown in custom‐made containers in a glasshouse. Plants were harvested when six leaves had fully expanded and encompassing angle of first flush of nodal roots (relative to vertical), leaf area, and root and shoot dry weight were determined for each plant. Nodal root angle ranged from 15 to 50° for inbred lines and 14 to 43° for hybrids and had a moderately high heritability (47%) in inbred lines. However, significant interaction between male and female parents in hybrids indicated significant SCA. Variation in nodal root angle was independent of variation in plant size (shoot and root weight and leaf area). Variability in plant size among hybrids was associated with the female parent (p < 0.001) and resulted in significant GCA. Screening and selection for nodal root angle should not be affected by potential differences in plant size between inbred lines and hybrids, although the significant SCA would limit predictability of root angle in hybrids based on the root angle of the parental inbred lines.

QTL mapping of root angle in F<sub>2</sub> populations from maize ‘B73’ × teosinte ‘<i>Zea luxurians</i>’

We evaluated variation in nodal root angle in the genus Zea and performed quantitative trait locus (QTL) mapping for the trait. Angle (in degrees) of roots emerging from the second (2nd-root angle) and third (3rd-root angle) nodes from the bottom of shoot showed wide variation in nine accessions; relatively high repeatability was obtained. QTL analyses controlling root angle were performed in the two sets of F2 populations (127 individuals in Trial A and 123 in Trial B) developed from different crossings of maize ‘B73’ (deep-rooting) × teosinte ‘Zea luxurians’ (shallow-rooting). In Trial A, we used an SSR-based map with 107 markers, covering 1,329 cM throughout all ten chromosomes. By composite interval mapping analysis, four QTLs were identified, two on chromosome 10 for 2nd-root angle and one each on chromosomes 2 and 7 for 3rd-root angle. In Trial B, using a 1,397 cM SSR-based map with 92 markers, one QTL was located on chromosome 4 and two on chromosome 7 for 2nd-root angle and one each on chromosomes 2, 4 and 7 for 3rd-root angle. The QTL on chromosome 7 (identified as Qra2nd3rd7.04) was consistently found across the trials. A potential role of the Qra2nd3rd7.04 in controlling angles of nodal roots and thus flooding tolerance was discussed.